The master cookbook

Every year, I look forward to teaching my biology classes the basics of molecular genetics, because it's just so cool.

All organisms on the Earth contain a master recipe book -- DNA -- that contains all of the instructions necessary to create them.  Each of those recipes is deciphered, through a pair of processes called transcription and translation; the first produces a temporary copy of a single recipe (called RNA), and the second takes that RNA and uses it to build a protein of some sort.  So to extend the analogy of DNA-as-cookbook; transcription would be photocopying a single recipe, and translation would be reading that recipe and using it to make lasagna.  (The lasagna, if you don't mind my stretching the analogy to the snapping point, would be the protein.)

The problem is, as with most things in life, it's not quite that simple.

Your DNA contains a lot more than recipes used in a straightforward fashion to the building of a protein.  Between twenty and seventy percent of your DNA -- depending on whom you believe -- is junk DNA, which are essentially evolutionary leftovers.  Genes that got damaged, lost promoters (promoters are, more or less, universal "on" switches), or were moved somewhere in the genome that they couldn't be activated.  Some researchers think that junk DNA provides a sort of backhanded benefit; it gives us a larger target for mutations.  Mutations in the junk DNA have no effect, so it makes it less likely that any given mutation will kill us.

But there are other complications, too.  Some DNA (called "non-coding DNA") doesn't actually produce proteins directly, but acts to control the activity of other genes -- so it's pretty critical even though it's not specifically making your lasagna for you.  Some of these are "riboswitches" -- bits of DNA that are transcribed into RNA, but the RNA then binds to other pieces of RNA and alters the rate at which they're translated.  Another example are the telomeres, which form the ends of the chromosomes and act to protect them from degradation -- the decreasing size of telomeres is thought to play a role in aging.  A third, more mysterious example are the VNTR (variable number tandem repeat) regions, which are regions made of the same pattern of bases repeated over and over -- it's been made useful in the technique of DNA fingerprinting in forensics, but their function in the living organism is unknown.

With all of this complexity, it's been an ongoing source of contention as to exactly how many genes we have.  As you can see from the admittedly brief description I've given, it's not completely clear whether something is a functional gene in the first place, so how could you hope for an accurate count?  Estimates have run up to 6.7 million genes in the human genome -- and it certainly seems like something as sophisticated as we are must surely be the product of a huge number of individual instructions.

But the more people have looked into it -- starting with the Human Genome Project in the 1990s -- the smaller the estimate has become.  Just last week, the most recent revision was released, and it's pretty startling; a team led by Steven Salzberg at Johns Hopkins University has come up with a tally of 21,306 coding genes (ones that directly produce proteins) and 21,856 non-coding genes (bits of DNA that act to control the expression of other genes).

Which, considering that we're made up of trillions of cells interacting in countless different ways, is really a pretty small number when you come to think about it.

Salzberg is up front that these estimates could still be revised.  He, and study co-author Mihaela Petrea, write:

We aligned all human genes from NCBI's RefSeq database to the Ensembl gene set in an attempt to explain the differences, but although the total counts differ by less than 300, there are several thousand genes in each set that do not map cleanly onto the other, many of them representing genes of unknown function.  Our personal best guess for the total number of human genes is 22,333, which corresponds to the current gene total at NCBI.  We prefer this to the slightly higher Ensembl gene count both because the NCBI annotation is slightly more conservative, and because recent compelling arguments support an even lower gene total.  This number could easily shrink or grow by 1,000 genes in the near future.  However, recent analyses make it clear that even if we agree on a complete list of human genes, any particular individual might be missing some of the genes in that list.  The genome sequence is complete enough now (although it is not yet finished) that few new genes are likely to be discovered in the gaps, but it seems likely that more genes remain to be discovered by sequencing more individuals.  Additional discoveries are likely to make our best estimates for this basic fact about the human genome continue to move up and down for many years to come.

So the exact count of recipes in our DNA cookbook is still a matter of contention, but the whole thing is fascinating -- to think that such a (relatively) small number of sets of instructions could produce something as complex as we are.  As for me, this whole discussion has left me hungry, for some reason.

I think I'm going to make some lasagna.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Tales of contagion

I have to admit to a morbid fascination with things that can kill you in nasty ways.

Tornadoes, hurricanes, earthquakes, mass extinctions from giant meteorite collisions -- and epidemics.  I remember first reading Daniel Defoe's A Journal of the Plague Year, about an outbreak of the Black Death in London in 1664 and 1665, when I was in college, and being simultaneously horrified and mesmerized at the scale of it.  An estimated 100,000 people died in two years -- a quarter of London's population.

But even that is dwarfed by two other epidemics.  First, there's the infamous outbreak of bubonic plague that started in 1347 and, by some estimates, killed one-third of the human population of the Earth -- something on the order of fifty million people.  The worst, though, was the "Spanish flu" epidemic of 1918 and 1919.  Odd that an event only a hundred years ago, and that killed an estimated 75 million people worldwide -- twice as many as World War I, which was happening at the same time -- is much less known.  Mention the Black Death, and almost everyone has an idea of what it is; mention the Spanish flu, and often all you get is a puzzled look.

Danse Macabre by Michael Wolgemut [image is in the Public Domain]

This all comes up because of a paper by Maria Spyrou et al. that appeared in Nature: Communications last week.  In it, the researchers describe looking for evidence of pathogens in the Bronze-Age burial sites -- and finding evidence that the bubonic plague has been with us for a long, long time.  The authors write:

The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics.  Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear.  Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia.  We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested.  Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.

Which is fascinating enough, but it bears mention that there are still a number of epidemics that scientists have no clear explanation for.  Here are three of the most puzzling:

1. "Sweating sickness."  In the late 15th and early 16th centuries, several waves of contagious illness swept through western Europe.  It killed fast -- starting with disorientation, fever, chills, aching joints, and finally progressing to delirium and copious sweating.  Most of the victims died within 36 hours of the onset.  It claimed a number of well-known victims, including Prince Arthur of England -- the son of King Henry VII, and brother of King Henry VIII.  Arthur's death at the age of fifteen put Henry in line for the throne, and set into motion events that would change the world -- such as the English Reformation and the founding of the Anglican Church.  Sweating sickness went as quickly as it started -- the last outbreak was in 1551, and it hasn't been seen since.  Scientists are still mystified as to the cause, but the speculation is it might have been a hantavirus, carried by mice.
2. The Dancing Plague of 1518.  In eastern France and western Germany, people were stricken by a disorder that caused shaking, mania, and... a desperation to dance.  People took to the streets, dancing desperately, many of them until they died of hunger, exposure, heat exhaustion, or stroke.  In Strasbourg alone, at the height of the plague, it was killing fifteen people a day.  It, like the sweating sickness, vanished as soon as it appeared, leaving everyone mystified as to its cause -- although some researchers suspect it might have been caused by ergot, a fungus that grows on wheat and rye and produces lysergic acid diethylamide -- LSD.
3. "Nodding syndrome."  This one is much more recent, having first emerged in the 1960s in Sudan.  It affects children, causing listlessness, stunting of growth (especially of the brain), and a peculiar symptom called a "nodding seizure," often triggered by eating or becoming cold.  The child's head bobs, and (s)he becomes unresponsive, the seizures lasting for up to ten or fifteen minutes.  It's progressive and fatal -- the usual duration being about three years.  To this day no one knows the cause, although some suspect it might be connected to parasitism by the roundworm Onchocercus volvulus, which is endemic in the area and also causes "river blindness."

So this combines my love of horrible things that can kill you with my love of unsolved mysteries.

Anyhow, I realize this is all kind of morbid, and I have no desire to ruin your mood.  After all, we live in an age where most of the worst diseases of antiquity have been vanished; even bubonic plague, if it's caught quickly, can be cured with antibiotics (and yes, there are still cases of it today).  Thankfully, we seem to have gotten rid of sweating sickness and the dancing plague, even if we've replaced them with Ebola fever and chikungunya and West Nile virus.  I'll still take what we've got today over life in the past, which was (accurately) described by Thomas Hobbes as "solitary, nasty, poor, brutish, and short."

Have a nice day.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

The justification merry-go-round

Today's post is about several links that all appeared in my inbox more or less simultaneously, and are even more interesting in juxtaposition.

First, let's look at the study that appeared this week in the European Journal of Social Psychology called "'They've Conspired against Us': Understanding the Role of Social Identification and Conspiracy Beliefs in Justification of Ingroup Collective Behaviour," authored by Maria Chayinska and Anca Minescu.  The gist of the research is that people jump into belief in conspiracy theories with the greatest of ease -- as long as such belief reinforces the behaviors of the social groups they already belonged to.

The study looked at 315 people in Ukraine, split between people who were supporters of the anti-Russian "Euromaidan" movement and ones who were against it. The researchers presented them with (false) conspiracy theories about the annexation of the Crimea by Russia, and looked at the degree to which they believed it without question.  The Euromaidan supporters were far more likely to accept the conspiracy theory that secret societies and evil plots were at work to sabotage the Ukrainian resistance movement.

Study co-author Maria Chayinska writes:

We found that supporters of a particular cause not only were prone to endorse specific conspiracy beliefs but also to use them in a blame game, thus justifying collective behavior of the group they identified with.  Contrarily, the opponents of the same cause were found not to endorse those beliefs at all.  Thus, we found how ideologically charged social identities align with the tendency to believe in particular conspiracy theories surrounding acute political and societal issues that commonly cause a divide in a public. 

Conspiracy theories are ideological in nature, so people who either strongly endorse or oppose them have a reason to do so.  This reason is oftentimes rooted in their psychological commitment and loyalty to particular social groups that advocate a certain ideology.

Which is an interesting, if not especially surprising, result.

The same day as a loyal reader of Skeptophilia sent me the above story, I received five -- count 'em, five -- links addressing the current practice of indefinite separation of children from parents who are attempting to immigrate to the United States.  Let's take them in order of least-to-most egregious:

First, Fox News's Tucker Carlson:

This is one of those moments that tells you everything about our ruling class.  They care far more about foreigners than about their own people.  You probably suspected that already.  [The Left's] only solution is immediate amnesty for anyone who crosses our borders with a minor in tow.  And of course, that's the same as no borders at all.

Well, if you think that everyone objecting to the horrid treatment of these children is a member of "the Left," you're including Ben Sasse, Susan Collins, Laura Bush, Bill Kristol, Ted Cruz, John McCain, and (for fuck's sake) Reverend Franklin Graham.  And Carlson's blatant straw man argument -- that Democrats are, one and all, for completely opening the borders to anyone -- is so idiotic it hardly deserves refutation.  (Allow me to say only that I defy you to find one elected official, left or right, who has proposed allowing unrestricted immigration.  Just one.)

Then there's Laura Ingraham, also (surprise!) of Fox News:

As more illegal immigrants are rushing the border, more kids are being separated from their parents.  And temporarily housed at what are, essentially, summer camps.

Lady, I don't know what kind of summer camp you attended as a kid, but I'm guessing it didn't require sleeping inside a locked cage.

Speaking of cages, there's Steve Doocy, of... guess where?:

While some have likened it to — them to concentration camps or cages, you do see that they have those thermal blankets, you do see some fencing, but keep in mind — some have referred to them as ‘cages,’ but, keep in mind, this is a great, big warehouse facility where they built walls out of chain link fences.

So not cages!  Just nice guest rooms!  With chain-link walls and cement floors!

Working our way up the nausea-induction scale, we have none other than Ann Coulter, who I honestly thought had decided she had better things to do than to vie for the 2018 Eva Braun Award, but I guess I was mistaken.  Here's what she said:

I get very nervous about the president getting his news from TV...  I would also say one other thing, these child actors weeping and crying on all the other networks 24/7 right now — do not fall for it, Mr. President...  A New Yorker article, the New Yorker is not a conservative publication, they describe how these kids, these kids are being coached.  They’re given scripts to read by liberals, according to the New Yorker.  Don’t fall for the actor children.

No worries!  The screams are all scripted!  Says so right in a non-existent article in the New Yorker!  (Maybe the kids are the same "crisis actors" the Deep State got to portray the victims of the Sandy Hook, Marjory Stoneman Douglas, and Boston Marathon massacres.  May as well reuse them, since it worked so well.)

But, if you can believe it, one person went beyond Ann Coulter, which I didn't even think was possible.  So if we can take one more turn on the justification merry-go-round, let's look at Christian television host and moderator of the podcast Faith & Freedom, Leigh Valentine.  The kids aren't actors, Valentine said; they're actually -- evil:

Immigrants crossing the border are committing rape after rape after rape.  Children below ten years old engaging in sexual activity — all kinds of sin and disgrace and darkness; the pit of the pits...  So we’re not getting the top-of-the-line echelon people coming over this border.  We’re getting criminals.  I mean, total criminals that are so debased and their minds are just gone.  They’re unclean, they’re murderers, they’re treacherous, they’re God-haters.

 Yup, that's a pretty sketchy bunch of debased, mindless criminal God-haters, right there.  [Image licensed under the Creative Commons Linda Hess Miller, Mesa Grande refugee camp 1987 116, CC BY 3.0]

Look, I'm not claiming I have an easy answer.  As I said earlier, I -- like damn near every left-leaning person in the United States -- am not proposing opening the borders and letting anyone in who wants to.  But the vast majority of these people are not criminals (and they fucking sure aren't actors, Ann Coulter).  They're people who are desperate because of awful conditions in their home countries, who want what all of us want -- a clean, comfortable place to live, enough food and water, and opportunities for their children.  Whatever the answer is, it is not demonizing them, dehumanizing them, and/or claiming that what they're going through is not so bad.

If you think a while, you might come up with a few instances in history where the people in power had precisely the same response to the plight of children being held in involuntary captivity.

None of those ended well.

What we are doing right now is wrong.  Pure and simple.  Separating children from their parents is immoral.  And don't start with me about under whose administration the practice started; that's entirely irrelevant.  It's happening now, and it's happening on a scale the likes of which we have never seen.

You stand up against it, or you have abandoned all claim to the moral high ground.

But it does make a weird sort of sense, in light of the Chayinska and Minescu paper we started with.  If you already believe that we're under siege, that immigrants are a threat to everything we hold dear, it's only a small leap to believing that the immigrant children themselves are to blame, or that the whole thing is some kind of grand conspiracy to destroy The American Way.

And all I can say is, if this is The American Way, I'm horrified at what our country has become.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Relics of a lost age

If I can be allowed to geek out a little, today's post is about two new discoveries in the field of paleontology.

The mid-Permian period was (1) a challenging time to live, when the climate was rapidly warming and drying, and (2) at 270 million years before the present, was a really long time ago.  Not only was the climate getting dicey, the world was heading for catastrophe -- the lockup of the supercontinent Pangaea, as all the world's land masses fused into one and the rest of the Earth was covered by a giant ocean, is thought to have been the kickoff to the largest wipeout the Earth has ever seen -- the Permian-Triassic extinction.  Not only did the formation of the supercontinent (and superocean) 252 million years ago drastically change the climate, the event coincided with the formation of the Siberian Traps, when four million cubic kilometers of basaltic lava flowed out over what is now eastern Russia.  The resulting massive burning of organic matter spiked the carbon dioxide content of the atmosphere, simultaneously causing the oxygen content to crash and triggering a warm-up that resulted in average ocean surface temperatures of 40 C (104 F).

The result: 95% of the species on Earth became extinct.

Of course, one of the lineages that made it through the bottleneck was our own ancestors.  Back in the mid-Permian -- pre-mass-extinction -- there was a group of protomammals called Gorgonopsians, which included some seriously scary carnivores (one, Inostrancevia, had a 45-centimeter-long skull and saber teeth -- preceding the more famous "saber-toothed tiger" Smilodon by a good 260 million years).

Permian protomammal fossils are quite rare, however.  So it's pretty awesome that paleontologist Christian Kammerer, paleontology curator of the North Carolina Museum of Natural Sciences, discovered fossils of not one, but two new species of mid-Permian protomammals in a small museum in Russia.

Called Gorynychus matsyutinae and Nochnitsa geminidens, the two were drastically different in size.  Gorynychus was probably one of the apex predators of its time, with a 25-centimeter-long skull and big, nasty, pointy teeth.  Nochnitsa, also a predator, was weasel-sized.  The genera were both named after beasts from Russian mythology -- the three-headed dragon Zmey Gorynych and the malevolent, vampiric night spirit Nochnitsa.

Artist's reconstruction of Gorynychus and Nochnitsa [by Matt Celeskey @clepsydrops, from the press release from the North Carolina Museum of Natural Sciences; used with permission]

These lineages both made it through the bottleneck, but not unscathed.  Their descendants, eighteen or so million years later, underwent some rapid evolution during the Permian-Triassic extinction, especially with respect to size.  "In the age before the dinosaurs, when protomammals were the dominant life on land, you had two different groups that switch off on which is the top predator," Kammerer said.  "You have wolf- to lion-sized saber tooth animals wiped out by a mass extinction, and [the Nochnitsa-like animals] take over.  But [Gorynychus-like animals] aren’t wiped out altogether in this extinction, and they take over and become a small insect eating predator, not large carnivores anymore."

Kammerer and his co-author (and co-discoverer of the fossils), Vladimir Matsyutin of the Vyatka Paleontological Museum of Kirov, Russia, were excited not only about having found fossils of two hitherto-unknown species, but about the potential for other discoveries tucked away in museums.  "I would guarantee you there are thousands of undescribed species in museum collections,” Kammerer said.  "Most new species are found in museum collections for the sole reason that there are literally millions of species on Earth today and many more in the fossil record.  When you’re going out and collecting specimens, you won’t know those things.  The people in the museum knew they were protomammals but they didn’t know they were new species."

So that's today's cool science story, about some of our (very) distant relatives.  I've always been fascinated with the early mammals -- for some reason, much more than the charismatic megafauna that were just getting their start at the same time (the dinosaurs, of course).  And the fact that these critters were out doing their thing as the Earth was heading toward the largest catastrophic extinction ever just adds a nice little frisson to the discovery.  You kind of want to warn them about what's coming, you know?

Oh, well, probably wouldn't have helped.  It's not like you can hide from four million cubic kilometers of lava.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Snake oil classification

As you may have noted, I have a serious problem with "alternative medicine" manufacturers who put on their bottles of snake oil, "Not intended to treat or cure any medical condition" when right on the bottle (in much larger print) it says that said snake oil will treat and/or cure a medical condition.

The disclaimer, for better or worse, apparently gets them off the hook if they're sued by someone who (for example) took homeopathic one-part-in-a-quintillion dilutions of weasel spit to cure their constipation and found themselves as plugged up as ever.  But it still bugs me, because however you slice it, these products are being touted as medicines, when in fact the vast majority of them are worthless -- and stop people from seeking out legitimate treatments that actually might work.

But now, the infamous "Goop" -- Gwyneth Paltrow's company that suggested, for example, that women with problems in their naughty bits should stick jade eggs into their vaginas (no, I'm not making this up) -- has come up with an even more sophisticated way not to take responsibility for the foolishness they peddle:

They've classified their products and "wellness" suggestions into different categories of foolishness.

I found this out from Dr. Jen Gunter's blog, which is a wonderful source of straight scoop about all things alt-med.  Dr. Gunter has gone all-out in fighting Gwyneth Paltrow's multi-million dollar health scam company, and what she uncovered this time is a doozy.  Here's how Paltrow is now dividing up her health products and recommendations:

• For Your Enjoyment: There probably aren’t going to be peer-reviewed studies about this concept, but it’s fun, and there’s real merit in that.
• Ancient Modality: This practice is nearly as old as time — many find value in it, even if modern-day research hasn’t caught up yet (it’s possible the practice will never attract its attention).
• Speculative but Promising: There’s momentum behind this concept, though it needs more research to elucidate exactly what’s at work.
• Supported by Science: There’s sound science for the value of this concept and the promise of more evidence to come soon that may prove its impact.
• Rigorously Tested: The validity of this concept is pretty much undisputed within the world of M.D.’s, D.O.’s, N.D.’s, and Ph.D.’s.

So they're conveniently leaving themselves an out if someone sues them.  "Ha ha," they can say.  "We labeled this one as 'for your enjoyment!'  There's real merit in the fact that you abandoned your chemotherapy for a coffee enema!  What fun!"

In the "speculative but promising" category, Gunter found such claims as drinking goat's milk to "rid yourself of parasites," and that eating apricots are "energy-shifting" and "transformative," but only if you eat them after three PM.  That's when their "energy-shifting" capacity is highest.

Because fruit, apparently, can tell time.

[Image is in the Public Domain]

Gunter, hearteningly, is having none of it.  She writes:

As far as I can tell with the GOOP rating system “enjoyment” means second-hand information from a ghost; “ancient” is code for biologically implausible, but sells well; and “speculative, but promising” is the fringe hypothesis of a naturopath or “Integrative” doctor.  I am pretty sure we won’t see too many “backed by science” posts because there aren’t many complementary products to sell alongside in the GOOP shoppe.

Because, after all, this is all about one thing: money.  Paltrow's quack cures and sham health aids are a multi-million dollar industry, and (as P. T. Barnum famously observed) there's a sucker born every minute.  Not only that, there's the even more unethical side of this; that some of her customers are people who have chronic diseases that are unresponsive even to the best medical care, or who are facing treatments that work but result in dreadful side effects (such as chemo and radiation therapy).  So out of desperation, and buoyed up by a false sense of hope from Paltrow's shtick, they buy what she's selling -- jeopardizing their own health, and in some cases, risking their lives.

If you think I'm overstating my case, check out the site What's the Harm?, which looks at specific instances of "alternative medicine" harming or killing patients.  The website is extensive; their header says they've found evidence of "368,379 people killed, 306,096 injured and over $2,815,931,000 in economic damages."

So I'm unimpressed by Paltrow's new system for classifying nonsense.  The fact is, if you're ill, you should seek out the help of a trained professional, not look for a cure from an actress who figured out that alternative medicine is one hell of a cash cow.  Regardless of how cleverly she markets her snake oil.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Illuminating a prison

In the unit on ethics in my Critical Thinking class, we always discuss a variety of experiments that have been done to elucidate the origins, characteristics, and extent of human morality.  Among the ones we look at are:

• Philippa Foot's famous "Trolly Problem" experiment (1967), where a person is presented with two scenarios, both of which result in one death to save five people -- but in one, the death is caused by an action with a mechanical intermediary (flipping a switch), while in the second, the death is caused by the person shoving someone off a bridge with their own hands.  The interesting result is that humans don't view these as equivalent -- having a mechanical intermediary far reduces the emotional charge of the situation, and makes people much more likely to do it, even though the outcomes are identical.
• The "Milgram experiment," conducted in 1963 by Stanley Milgram, which looked at the likelihood of someone hurting another person if commanded to do so by an authority figure.  Turns out, most of us will...
• The Zurich tribalism experiment, done in Switzerland in 2015, wherein we find test subjects are willing to inflict painful shocks on others without activating their own empathy centers -- if the person being shocked is wearing a soccer jersey of a team the test subject didn't like.
• Karen Wynn's "baby lab" experiment (2014), which found that even very young babies have an innate perception of fairness and morality, and want helpful individuals rewarded and unhelpful individuals punished.

The last time I taught the class, I included a fifth experiment -- the notorious "Stanford prison experiment," done by Philip Zimbardo in 1971.  You've probably heard about this one; it involved 24 Stanford students who had all undergone personality screening to weed out anyone with a tendency toward sociopathy.  The 24 were split into two groups -- the "prisoners" and the "guards."  As Zimbardo recounted the outcome, the guards very quickly banded together and acted with cruelty and disdain toward the prisoners, and the prisoners responded by sabotaging whatever they could.  Several of the prisoners broke down completely, and the experiment had to be called off because some of the prisoners were obviously in such mental distress that it would have been inhumane to continue.

Sing Sing Prison, 1915 [Image is in the Public Domain]

Zimbardo became famous instantly, and his results used to explain everything from people who'd been collaborators during the Holocaust to William Calley and his men and the perpetration of the My Lai Massacre.  When banding together against a perceived common enemy, Zimbardo said, we'll be much more likely to behave immorally -- especially when (as the Milgram experiment suggests) we're being ordered to behave that way by an authority.

There are two problems with this.

First, in 2001, psychologists Alex Haslam and Stephen Reicher tried to replicate Zimbardo's results, and found that it didn't work.  What they suggested was that the outcome of the Stanford prison experiment weren't because the "guards" saw the "prisoners" as enemies, but because the guards were identifying with the experimenters -- in other words, their activities were being directed by an authority figure.  So the experiment boils down to a rehash of what Milgram did eight years earlier.

But there's a darker side of this, which I just found out about in an article in Medium by Ben Blum called "The Lifespan of a Lie."  In it, Blum makes a disturbing claim; that Zimbardo hadn't done what he claimed, which was to break the students into groups randomly and give them no instructions other than "guards control prisoners, prisoners obey guards;" he had actually coached the guards to behave cruelly -- and may have even encouraged one of the prisoners to go into hysterics.

The most famous breakdown, that of "prisoner" Doug Korpi, was dramatic -- he was locked in a closet by a guard, and proceeded to have a complete meltdown, screaming and crying and kicking the door.  The problem, Korpi says, is that it was all an act, and both he and Zimbardo knew it.  "Anybody who is a clinician would know that I was faking,” Korpi told Blum.  "If you listen to the tape, it’s not subtle.  I’m not that good at acting.  I mean, I think I do a fairly good job, but I’m more hysterical than psychotic."

At least some of the guards were acting as well.  One of the ones that had (according to Zimbardo) exhibited true cruelty toward the prisoners, Dave Eshelman, said his whole persona was a put-on.  "I took it as a kind of an improv exercise,” Eshelman told Blum.  "I believed that I was doing what the researchers wanted me to do, and I thought I’d do it better than anybody else by creating this despicable guard persona.  I’d never been to the South, but I used a southern accent, which I got from Cool Hand Luke."

Zimbardo, of course, denies all of this, and spoke to Blum briefly -- mostly to say that the experiment was fine, and the claims of fraud all nonsense.  Instead, he said that Haslam and Reicher's failed attempt at replication was "fraudulent," and the experiment itself valid.  "It’s the most famous study in the history of psychology at this point," Zimbardo told Blum.  "There’s no study that people talk about fifty years later.  Ordinary people know about it.  They say, ‘What do you do?’ ‘I’m a psychologist.’  It could be a cab driver in Budapest.  It could be a restaurant owner in Poland.  I mention I’m a psychologist, and they say, ‘Did you hear about the study?’  It’s got a life of its own now.  If he wants to say it was all a hoax, that’s up to him.  I’m not going to defend it anymore.  The defense is its longevity."

Which, of course, is not much of a defense.  Some really stupid ideas (I'm lookin' at you, homeopathy) have been around for ages.  I do find it rather upsetting, though, and not just because I've been teaching an experiment for years that turns out not to have gone down the way the researchers claimed.  It's a stain on science as a whole -- that we accepted the results of an experiment that failed replication, mostly because its outcome seemed so comforting.  People aren't inherently immoral; they act immorally when they're placed in situations where it's expected.  Alter situations, it implied, and people will rise to higher motives.

Well, maybe.  There are still a lot of questions about morality, and the other four experiments I teach have borne up to scrutiny.  We do harm more easily when we're one step removed from the person being harmed, when an authority figure tells us to, when the harmed person doesn't belong to our "tribe," and when the recipient of punishment is perceived to have deserved it.  But simply banding together, Lord of the Flies-style, to visit harm upon the helpless -- the evidence for that is far slimmer.

And I suppose the Zimbardo experiment will have to be transferred to a different lecture next year -- the one I do on examples of scientific fraud and researcher malfeasance.

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This week's Skeptophilia book recommendation is a classic: the late Oliver Sacks's The Man Who Mistook His Wife for a Hat.  It's required reading for anyone who is interested in the inner workings of the human mind, and highlights how fragile our perceptual apparatus is -- and how even minor changes in our nervous systems can result in our interacting with the world in what appear from the outside to be completely bizarre ways.  Broken up into short vignettes about actual patients Sacks worked with, it's a quick and completely fascinating read.

Follow the compass needle

I have to resist the temptation of scoffing too quickly, but sometimes it turns out to be justified.

This comes up because of an article from Body Ecology called "Could the Direction You Sleep In Improve Your Health and Well-Being?" that a loyal reader of Skeptophilia sent me yesterday.  The contention of the article is that should never sleep with your head pointing north or west; east or south is best.  Fail to follow this advice, and you're seriously risking getting some horrible disease.  It then goes into some "Eastern medicine" goofiness and stuff about "feng shui" that has no scientific validity whatsoever.

The article states, cheerfully, "[S]cience and eastern medicine both agree" that sleep direction makes a difference, a claim that made me snort derisively.

But one thing caught my eye, which is that the article said there's been a study -- a real study, not some hand-waving mystical nonsense -- that showed people who sleep oriented north/south have shorter periods of REM (rapid-eye movement) sleep than people oriented east/west.  There was no link provided, nor even a mention of where or by whom the study had been conducted, but I thought I'd give the author the benefit of the doubt and try to track it down.

[Image licensed under the Creative Commons Evgeniy Isaev from Moscow, Russia, Sleeping man. (7174597014), CC BY 2.0]

After some digging, I found the paper they were referencing.  It was from way back in 1987, and was written by three scientists in Germany, one at the Max Planck Institute, and the other two at the University of Munich.  Entitled, "Dependence of a Sleeping Parameter from the N-S or E-W Sleeping Direction," wherein eight male subjects were subjected to EEGs for eight nights each, alternating nights while sleeping oriented north/south with nights oriented east/west.  The authors write:

The only significant difference occurred in REM latency which was 5.5 min shorter in E-W direction (p< 0.02).  Other sleep parameters which could be interpreted as stress parameters (sleep latency, intermittent awakenings, percentage of stage 1, stageshifts, movement times) were not different between the two positions.  The same goes for the other parameters.

So the Body Ecology got the facts wrong; the north/south sleepers didn't REM less, they had longer REM latency -- the time from the onset of sleep to the first episode of REM.  And that was only by five and a half minutes.  In fact, there was a great deal more difference between the REM latency of all the subjects for the first four versus the second four nights, regardless of what direction they were oriented -- a difference of 22 minutes.

Nevertheless, the authors conclude hopefully:

The adaption effects are balanced out by the fact that two paired subjects slept always in different directions. The fact that among the sleep parameters REM latency is affected by the position of the bed... seems to support our interpretation because mainly REM latency reacts to external influences. Therefore the most probable interpretation of our observation is the assumption that the geomagnetic field influences humans differently depending on their positions relative to the field direction.

I'm no statistician, but it seems to me that eight subjects studied for eight nights, resulting in a difference in REM latency of five and a half minutes and no other significant changes, is pretty weak evidence that there's anything to see here.  It's also significant that the article was published in 1987 -- and I couldn't find a single other study of the claim since that time.

The piece in Body Ecology also mentions a second study (once again, no link) claiming that other mammal species respond to the Earth's magnetic field.  That's not so far-fetched; it's known that many bird species exhibit magnetotaxis, which is orientation based on an internal compass.  (This was discovered by a study way back in 1971 done right here at Cornell University.)  But the mammals claim was new to me, and appears to come from a 2008 study at the University of Duisberg-Essen (Germany) claiming that satellite images of herds of deer and cattle showed that they preferentially oriented their bodies north/south.  The authors don't bother to speculate as to why they would do this, and claim to have controlled for such factors as prevailing wind direction and the angle of the sun.  But a 2011 study tried to replicate the results and failed -- there was no preferred orientation.  Cattle and deer did pretty much what you'd expect they'd do, which is stand around eating stuff facing any way that happens to be convenient.

Of course, weirder things have been claimed.  A 2013 paper in Frontiers of Zoology said that a two-year study of dogs showed that they preferred to poop while aligned north/south.  Which raises a question: who even thought of looking into this idea?  I mean, thinking outside the box is one thing, but this is a bizarre question to ask.  Maybe the scientists, like me, tire of having their dogs turn in circles 832 times before relieving themselves, and wanted to know why they were doing it.

Unsurprisingly, this study was questioned, too, most rigorously by Duncan Forgan over at Research the Headlines, who had the following to say:

On the other hand, the dog’s magnetoception (if it possesses it) does not appear to be particularly effective in general.  When the researchers pooled all the data (calm and not-calm magnetic fields), they saw no evidence of alignment at all, meaning that dogs can only rely on this sense if the magnetic field behaves itself, which only happened during around a third of the researcher’s observations. 

It also means that if you own a dog, you are probably unlikely to notice any alignment, unless you’re willing to only note your pup’s pooping practices when you’ve previously measured a stable magnetic field.

An experiment which, frankly, I am not nearly interested enough to carry out.

Anyhow.  It looks like my scornful reaction to the original article is more or less warranted, and any evidence that humans respond behaviorally (or any other way) to the Earth's magnetic field is questionable at best.  If it floats your boat to turn your bed so your head is facing east, knock yourself out, but I'm guessing any difference you notice will be because you expected there to be a change -- i.e., the placebo effect.

For what it's worth, though, I sleep with my head pointing north, and I'm a notorious insomniac.  It's only one data point, but make of it what you will.

******************************

This week's Skeptophilia book recommendation is a classic: the late Oliver Sacks's The Man Who Mistook His Wife for a Hat.  It's required reading for anyone who is interested in the inner workings of the human mind, and highlights how fragile our perceptual apparatus is -- and how even minor changes in our nervous systems can result in our interacting with the world in what appear from the outside to be completely bizarre ways.  Broken up into short vignettes about actual patients Sacks worked with, it's a quick and completely fascinating read.